Editing causes book pages to drop out of the outline

I have been trying to upgrade from 5.21 to 6.15, on a Linux server running Apache 2.2.14 and PHP 5.2.11. When I first attempted the upgrade, I got an error (#533522: Update problems 5 to 6 with book module...) running update.php on the book module. Eventually, I used Node Convert to turn all my book pages into another content type, disabled and uninstalled book.module, reinstalled book.module, converted the relevant nodes back to book pages, and rebuilt my book structure (about 100 book pages in 3 books) one page at a time. Tedious, but it seemed to work for the time being.

However, if I then edit a book page, it appears to fall out of the book outline. If I am viewing that particular page, it shows up as a top-level book in the book navigation menu, even if it was a child page before, but if I navigate to a different book, the book page that I just edited does not appear in the book navigation menu anymore. However, if I return to the edited book page and go to the "Outline" tab, the page claims to still be a part of the book it was originally in, but its parent is the top-level page of that book, regardless of the original depth of the book page in question. If the book page that was modified had any children, they remain children of that page, but their Outline tab also indicates that they are a child of the top-level page of the original book.

To illustrate, suppose we have the following hierarchy:

• Sample Book
• • Chapter
  • • Section
    • • Subsection

and we then edit the "Section" page. If we are at the "Section" page, "Subsection" will show up as its child in the navigation links at the bottom of the page, but there will be no option to navigate "up". The Book Navigation menu will look like:

• Sample Book
• Section
• • Subsection

Note that "Section" shows up as a top-level book page in the navigation block. If we then navigate to "Chapter," the Book Navigation menu will look like:

• Sample Book
• • Chapter

With "Section" appearing nowhere in the block. If we return to "Section" and view the Outline tab, we will see:

Book: Sample Book
Parent item: Sample Book

The same items are shown if we view the Outline tab for "Subsection," even though the navigation links place "Subsection" as a child of "Section." If we return to the Outline tab for "Section" and change the parent item to "Chapter," then the desired hierarchy and functionality is restored; the parent item for "Subsection" automatically changes back to "Section"

The above behavior only occurs with the pre-existing (converted) book pages; any newly created book pages stay in place in the outline when they are edited.

I have a number of contrib modules enabled, but the one that seems most relevant is Node Relativity, as I have had some minor issues with book page child links showing up as Node Relativity relationships in 5.21. In particular, I had some Node Relativity-enabled custom content types whose nodes were also (deliberately) placed into book outlines, which led to newly created book pages elsewhere being treated as children under Node Relativity. The other contrib modules include CCK (+ several CCK modules, none of which have been added to book pages), Pathologic, Advanced Help, Automatic Nodetitles, Custom Breadcrumbs, MimeDetect, Node Convert, Pathauto, Token, jQuery Update, Wysiwyg, and Views.